“Is Alternative” option is only available in Quotations because it is used to offer different item choices to customers. By the time you get to Sales Orders, Delivery Notes, and Sales Invoices, the items should be final. Adding alternatives at these stages could cause confusion and problems with inventory and billing.
However, you can customize these doctype to include an “Is Alternative” checkbox if you need it, but it is very tricky to manage on the inventory side because you also have to override some inventory-related methods.